Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the under...

While Kolmogorov complexity is the accepted absolute measure of information content in an individual finite object, a similarly absolute notion is needed for the information distance between two individual objects, for example, two pictures. We give several natural definitions of a universal information metric, based on length of shortest programs for either ordinary computations or reversible ...

The thermodynamic behaviour of self-gravitating N -body systems has been worked out by borrowing a standard method from Molecular Dynamics: the time averages of suitable quantities are numerically computed along the dynamical trajectories to yield thermodynamic observables. The link between dynamics and thermodynamics is made in the microcanonical ensemble of statistical mechanics. The dynamics...

We present a hybrid computational methodology to predict multiple energetically accessible conformations for G protein-coupled receptors (GPCRs) that might play a role in binding to ligands and different signaling partners. To our knowledge, this method, termed ActiveGEnSeMBLE, enables the first quantitative energy profile for GPCR activation that is consistent with the qualitative profile dedu...

Recent studies show the Earth’s core may contain more magnesium (Mg) than previously thought, with perhaps up to 6 wt% in the early core and ∼1wt% still existing now. The Mg partitioning between liquid and solid iron (Fe) under the relevant conditions is needed, therefore, in order to establish whether the presence of magnesium will have an effect on core properties, particularly those of the i...

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck-Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER...

Bayesian inference is intractable for many interesting models, making deterministic algorithms for approximate inference highly desirable. Unlike stochastic methods, which are exact in the limit, the accuracy of these approaches cannot be reasonably judged. In this paper we show how low order perturbation corrections to an expectation-consistent (EC) approximation can provide the necessary tool...

Smart surfaces of biobased materials: IV. Dynamic surface effects in films of F-containing cellulose esters Ulrike Becker and Wolfgang Glasser Biobased Materials/Recycling Center, and Department of Wood Science and Forest Products Virginia Tech, Blacksburg, VA Abstract: Dynamic surface phenomena were examined in films of fluorine (F)-containing cellulose derivatives. The derivatives were either...

We determine the relative thermodynamic stability of competing homogeneously and inhomogeneously ordered ferroelectric phases of PbTiO3 using its free-energy landscape, obtained from constrained-polarization moleculardynamics simulations with a first-principles effective Hamiltonian and thermodynamic integration. While we find that the tetragonal structure is thermodynamically most stable at te...

The ability to determine the free energy of solvation for a number of small organic molecules with varying sizes and properties from the coordinate trajectory of a single simulation of a given reference state was investigated. The relative free energies were estimated from a single step perturbation using the perturbation formula. The reference state consisted of a cavity surrounded by solvent....